Abstract Cancer continues to pose a substantial global health challenge, driving the need for new and innovative therapeutic strategies. Among these, photothermal therapy (PTT) has gained attention for its potential. This approach utilizes nanoparticles (NPs) to selectively target and destroy cancer cells, presenting a promising avenue for treatment. This study introduces a rapid, one pot and green synthesis method for synthesizing stable and biocompatible gold nanoparticles (AuNPs) using quercetin, a naturally occurring flavonoid, as both a reducing and stabilizing agent. The sonochemical synthesis of AuNPs employing quercetin not only ensures efficient synthesis but also enhances their stability and biocompatibility, critical for effective PTT against cancer cells. Fourier transform infrared analysis reveals molecular interactions between quercetin and AuNPs, elucidating their conjugation and functionalization. Furthermore, cytotoxicity assays demonstrate the biocompatibility of the synthesized AuNPs, encouraging further investigation into their photothermal efficacy. In vitro photothermal ablation experiments demonstrate the potential of quercetin-mediated AuNPs to induce photoinduced thermal damage to cancer cells under near-infrared laser irradiation. The study also reports a negative zeta potential value (− 35 mV) for the synthesized AuNPs, indicating adequate colloidal stability, and TEM analysis reveals spherical nanoparticles with an average size ranging from 19 to 25 nm. This study presents a simple yet impactful approach for synthesizing AuNPs with enhanced stability and biocompatibility, paving the way for advanced applications in cancer therapy. Graphical abstract